Sample Resequencing Stats

Note: The mutation counts shown below represent unfiltered mutation sets.

ALE, Flask, Isolate	Predicted Mutations	Mean Coverage	Total Reads	Percent Mapped	Mapped Reads	Average Read Length
A5 F1 I1 R1	770	51.4	2439994	93.8%	2288714	110.3

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,619,957	G→A	128 (TAG→TAA)	marA →	multiple antibiotic resistance transcriptional regulator

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,619,957	0	G	A	100.0%	142.1 / NA	45	128 (TAG→TAA)	marA	multiple antibiotic resistance transcriptional regulator
Reads supporting (aligned to +/- strand): ref base G (0/0); new base A (24/21); total (24/21)

CTTCGAGTCGCAACAAACTCTGACCCGAACCTTCAAAAATTACTTTGATGTTCCGCCGCATAAATACCGGATGACCAATATGCAGGGCGAATCGCGCTTTTTACATCCATTAAATCATTACAACAGCTAGTTGAAAACGTGACAACGTCACTGAGGCAATCATGAAACCACTTTCATCCGCAATAGCAGCTGCGCTTATTCTC‑TTTTCCGCGCAGGGCGTTGCGGAACAAACCACGCAGCCAGTTGTTACTTCTTGTGCCAATG  >  NC_000913/1619828‑1620091

cTTCGAGTCGCAACAAACTCTGACCCGAACCTTCAAAAATTACTTTGATGTTCCGCCGCATAAATACCGGATGACCAATATGCAGGGCGAATCGCGCTTTTTACATCCATTAAATCATTACAACAGCTAATTGAAAACg                                                                                                                                >  1:397582/1‑139 (MQ=255)

    gAGTCGCAACAAACTCTGACCCGAACCTTCAAAAATTACTTTGATGTTCCGCCGCATAAATACCGGATGACCAATATGCAGGGCGAATCGCGCTTTTTACATCCATTAAATCATTACAACAGCTAATTGAAAACGTGAc                                                                                                                            >  1:1138534/1‑139 (MQ=255)

                  tctGACCCGAACCTTCAAAAATTACTTTGATGTTCCGCCGCATAAATACCGGATGACCAATATGCAGGGCGAATCGCGCTTTTTACATCCATTAAATCATTACAACAGCTAATTGAAAACGTGACAACGTCACTGAGGc                                                                                                              <  1:236864/139‑1 (MQ=255)

                    tGACCCGAACCTTCAAAAATTACTTTGATGTTCCGCCGCATAAATACCGGATGACCAATATGCAGGGCGAATCGCGCTTTTTACATCCATTAAATCATTACAACAGCTAATTGAAAACGTGACAACGTCACTGAGGCaa                                                                                                            >  1:821011/1‑139 (MQ=255)

                       cccGAACCTTCAAAAATTACTTTGATGTTCCGCCGCATAAATACCGGATGACCAATATGCAGGGCGAATCGCGCTTTTTACATCCATTAAATCATTACAACAGCTAATTGAAAACGTGACAACGTCACTGAGGCAATCa                                                                                                         >  1:301460/1‑139 (MQ=255)

                               ttCAAAAATTACTTTGATGTTCCGCCGCATAAATACCGGATGACCAATATGCAGGGCGAATCGCGCTTTTTACATCCATTAAATCATTACAACAGCTAATTGAAAACGTGACAACGTCACTGAGGCAATCATGAAACCa                                                                                                 <  1:999056/139‑1 (MQ=255)

                                    aaaTTACTTTGATGTTCCGCCGCATAAATACCGGATGACCAATATGCAGGGCGAATCGCGCTTTTTACATCCATTAAATCATTACAACAGCTAATTGAAAACGTGACAACGTCACTGAGGCAATCATGAAACCACTTTc                                                                                            <  2:821011/139‑1 (MQ=255)

                                                  ttCCGCCGCATAAATACCGGATGACCAATATGCAGGGCGAATCGCGCTTTTTACATCCATTAAATCATTACAACAGCTAATTGAAAACGTGACAACGTCACTGAGGCAATCATGAAACCACTTTCATCCGCAATagcag                                                                              >  2:87452/1‑139 (MQ=255)

                                                     cgccgcATAAATACCGGATGACCAATATGCAGGGCGAATCGCGCTTTTTACATCCATTAAATCATTACAACAGCTAATTGAAAACGTGACAACGTCACTGAGGCAATCATGAAACCACTTTCATCCGCAATAGCAGCTg                                                                           >  1:833457/1‑139 (MQ=255)

                                                        cgcATAAATACCGGATGACCAATATGCAGGGCGAATCGCGCTTTTTACATCCATTAAATCATTACAACAGCTAATTGAAAACGTGACAACGTCACTGAGGCAATCATGAAACCACTTTCATCCGCAATAGCAGCTgcgc                                                                        <  2:397582/139‑1 (MQ=255)

                                                        cgcATAAATACCGGATGACCAATATGCAGGGCGAATCGCGCTTTTTACATCCATTAAATCATTACAACAGCTAATTGAAAACGTGACAACGTCACTGAGGCAATCATGAAACCACTTTCATCCGCAATAGCAGCTgcgc                                                                        <  2:1138534/139‑1 (MQ=255)

                                                             aaaTACCGGATGACCAATATGCAGGGCGAATCGCGCTTTTTACATCCATTAAATCATTACAACAGCTAATTGAAAACGTGACAACGTCACTGAGGCAATCATGAAACCACTTTCATCCGCAATAGCAGCTGCGCTTAtt                                                                   <  1:636494/139‑1 (MQ=255)

                                                                     gATGACCAATATGCAGGGCGAATCGCGCTTTTTACATCCATTAAATCATTACAACAGCTAATTGAAAACGTGACAACGTCACTGAGGCAATCATGAAACCACTTTCATCCGCAATAGCAGCTGCGCTTATTCTC‑TTTTc                                                          >  2:370469/1‑139 (MQ=255)

                                                                     gATGACCAATATGCAGGGCGAATCGCGCTTTTTACATCCATTAAATCATTACAACAGCTAATTGAAAACGTGACAACGTCACTGAGGCAATCATGAAACCACTTTCATCCGCAATAGCAGCTGCGCTTATTCTC‑TTTTc                                                          >  2:235226/1‑139 (MQ=255)

                                                                       tGACCAATATGCAGGGCGAATCGCGCTTTTTACATCCATTAAATCATTACAACAGCTAATTGAAAACGTGACAACGTCACTGAGGCAATCATGAAACCACTTTCATCCGCAATAGCAGCTGCGCTTATTCTC‑TTTTCcg                                                        >  2:687572/1‑139 (MQ=255)

                                                                         aCCAATATGCAGGGCGAATCGCGCTTTTTACATCCATTAAATCATTACAACAGCTAATTGAAAACGTGACAACGTCACTGAGGCAATCATGAAACCACTTTCATCCGCAAt                                                                                   >  2:8452/1‑111 (MQ=255)

                                                                         aCCAATATGCAGGGCGAATCGCGCTTTTTACATCCATTAAATCATTACAACAGCTAATTGAAAACGTGACAACGTCACTGAGGCAATCATGAAACCACTTTCATCCGCAAt                                                                                   <  1:8452/111‑1 (MQ=255)

                                                                         aCCAATATGCAGGGCGAATCGCGCTTTTTACATCCATTAAATCATTACAACAGCTAATTGAAAACGTGACAACGTCACTGAGGCAATCATGAAACCACTTTCATCCGCAATAGCAGCTGCGCTTATTCTC‑TTTTCcgcg                                                      <  1:52577/139‑1 (MQ=255)

                                                                             atatGCAGGGCGAATCGCGCTTTTTACATCCATTAAATCATTACAACAGCTAATTGAAAACGTGACAACGTCACTGAGGCAATCATGAAACCACTTTCATCCGCAATAGCAGCTGCGCtt                                                                      <  2:792815/120‑1 (MQ=255)

                                                                             atatGCAGGGCGAATCGCGCTTTTTACATCCATTAAATCATTACAACAGCTAATTGAAAACGTAACAACGTCACTGAGGCAATCATGAAACCACTATCATCCGCAATAGCAGCTGCGCtt                                                                      >  1:792815/1‑120 (MQ=255)

                                                                                     ggCGAATCGCGCTTTTTACATCCATTAAATCATTACAACAGCTAATTGAAAACGTGACAACGTCACTGAGGCAATCATGAAACCACTTTCATCCGCAATAGCAGCTGCGCTTATTCTC‑TTTTCCGCGCa                                                    >  2:1130122/1‑129 (MQ=255)

                                                                                     ggCGAATCGCGCTTTTTACATCCATTAAATCATTACAACAGCTAATTGAAAACGTGACAACGTCACTGAGGCAATCATGAAACCACTTTCATCCGCAATAGCAGCTGCGCTTATTCTC‑TTTTCCGCGCa                                                    <  1:1130122/129‑1 (MQ=255)

                                                                                          aTCGCGCTTTTTACATCCATTAAATCATTACAACAGCTAATTGAAAACGTGACAACGTCACTGAGGCAATCATGAAACCACTTTCATCCGCAATAGCAGCTGCGCTTATtct                                                                 <  1:409211/112‑1 (MQ=255)

                                                                                          aTCGCGCTTTTTACATCCATTAAATCATTACAACAGCTAATTGAAAACGTGACAACGTCACTGAGGCAATCATGAAACCACTTTCATCCGCAATAGCAGCTGCGCTTATtct                                                                 >  2:409211/1‑112 (MQ=255)

                                                                                          aTCGCGCTTTTTACATCCATTAAATCATTACAACAGCTAATTGAAAACGTGACAACGTCACTGAGGCAATCATGAAACCACTTTCATCCGCAATAGCAGCTGCGCTTATTCTCTTTTTCCGCGCAGGGCGTTGCGGAAc                                      >  1:763780/1‑139 (MQ=255)

                                                                                          aTCGCGCTTTTTACATCCATTAAATCATTACAACAGCTAATTGAAAACGTGACAACGTCACTGAGGCAATCATGAAACCACTTTCATCCGCAATAGCAGCTGCGCTTATTCTC‑TTTTCCGCGCAGGGCGTTGCGGAACa                                     >  2:518491/1‑139 (MQ=255)

                                                                                                 tttttACATCCATTAAATCATTACAACAGCTAATTGAAAACGTGACAACGTCACTGAGGCAATCATGAAACCACTTTCATCCGCAATAGCAGCTGCGCTTATTCTC‑TTTTCCGCGCAGGGCGTTGCGGAACAAACCACg                              <  2:948780/139‑1 (MQ=255)

                                                                                                    ttACATCCATTAAATCATTACAACAGCTAATTGAAAACGTGACAACGTCACTGAGGCAATCATGAAACCACTTTCATCCGCAATAGCAGCTGCGCTTATTCTC‑TTTTCCGCGCAGGGCGTTGCGGAACAAACCACGCAg                           <  1:235226/139‑1 (MQ=255)

                                                                                                     tACATCCATTAAATCATTACAACAGCTAATTGAAAACGTGACAACGTCACTGAGGCAATCATGAAACCACTTTCATCCGCAATAGCAGCTGCGCTTATTCTCTTTTTCCGCGCAGGGCGTTGCGGAACAAACCACGCAg                           <  2:763780/139‑1 (MQ=255)

                                                                                                     tACATCCATTAAATCATTACAACAGCTAATTGAAAACGTGACAACGTCACTGAGGCAATCATGAAACCACTTTCATCCGCAATAGCAGCTGCGCTTATTCTC‑TTTTCCGCGCAGGGCGTTGCGGAACAAACCACGCAGc                          <  1:87452/139‑1 (MQ=255)

                                                                                                          ccATTAAATCATTACAACAGCTAATTGAAAACGTGACAACGTCACTGAGGCAATCGTGAAACCACTTTCATCCGCAATAGCAGCTGCGCTTATTCTC‑TTTTCCGCGCAGGGCGTTGCGGAACAAACCACGCAGCCAgtt                     <  2:1033325/139‑1 (MQ=255)

                                                                                                             ttAAATCATTACAACAGCTAATTGAAAACGTGACAACGTCACTGAGGCa                                                                                                             >  1:52174/1‑49 (MQ=255)

                                                                                                             ttAAATCATTACAACAGCTAATTGAAAACGTGACAACGTCACTGAGGCa                                                                                                             <  2:52174/49‑1 (MQ=255)

                                                                                                             ttAAATCATTACAACAGCTAATTGAAAACGTGACAACGTCACTGAGGCAATCATGAAACCACTTTCATCCGCAATAGCAGCTGCGCTTATTCTC‑TTTTCCGCGCAGGGCGTTGCGGAACAAACCACGCAGCCAgttgtt                  >  2:560754/1‑139 (MQ=255)

                                                                                                                      tACAACAGCTAATTGAAAACGTGACAACGTCACTGAGGCAATCATGAAACCACTTTCATCCGCAATAGCAGCTGCGCTTATTCTC‑TTTTCCGCGCAGGGCGTTGCGGAACAAACCACGCAGCCAGTTGTTACTTCTtgt         >  1:1212358/1‑139 (MQ=255)

                                                                                                                       acaacaGCTAATTGAAAACGTGACAACGTCACTGAGGCAATCATGAAACCACTTTCATCCGCAATAGCAGCTGCGCTTATTCTC‑TTTTCCGCGCAGGGCGTTGCGGAACAAACCACGCAGCCa                        <  1:776376/123‑1 (MQ=255)

                                                                                                                       acaacaGCTAATTGAAAACGTGACAACGTCACTGAGGCAATCATGAAACCACTTTCATCCGCAATAGCAGCTGCGCTTATTCTC‑TTTTCCGCGCAGGGCGTTGCGGAACAAACCACGCAGCCa                        >  2:776376/1‑123 (MQ=255)

                                                                                                                           caGCTAATTGAAAACGTGACAACGTCACTGAGGCAATCATGAAACCACTTTCATCCGCAATAGCAGCTGCGCTTATTCTC‑TTTTCCGCGCAGGGCGTTGCGGAACAAACCACGCAGCCAg                       >  1:22344/1‑120 (MQ=255)

                                                                                                                           caGCTAATTGAAAACGTGACAACGTCACTGAGGCAATCATGAAACCACTTTCATCCGCAATAGCAGCTGCGCTTATTCTC‑TTTTCCGCGCAGGGCGTTGCGGAACAAACCACGCAGCCAg                       <  2:22344/120‑1 (MQ=255)

                                                                                                                           caGCTAATTGAAAACGTGACAACGTCACTGAGGCAATCATGAAACCACTTTCATCCGCAATAGCAGCTGCGCTTATTCTC‑TTTTCCGCGCAGGGCGTTGCGGAACAAACCACGCAGCCAGTTGTTACTTCTTGTGCCaa    <  1:560754/139‑1 (MQ=255)

                                                                                                                            aGCTAATTGAAAACGTGACAACGTCACTGAGGCAATCATGAAACCACTTTCATCCGCAATAGCAGCTGCGCTTATTCTC‑TTTTCCGCGCAGGGCGTTGCGGAACAAACCACGCAGCCAGTTGTTACTTCTTGTGCCAAt   >  2:252053/1‑139 (MQ=255)

                                                                                                                             gCTAATTGAAAACGTGACAACGTCACTGAGGCAATCATGAAACCACTTTCATCCGCAATAGCAGCTGCGCTTATtct                                                                 <  2:1119089/77‑1 (MQ=255)

                                                                                                                             gCTAATTGAAAACGTGACAACGTCACTGAGGCAATCATGAAACCACTTTCATCCGCAATAGCAGCTGCGCTTATtct                                                                 >  1:1119089/1‑77 (MQ=255)

                                                                                                                             gCTAATTGAAAACGTGACAACGTCACTGAGGCAATCATGAAACCACTTTCATCCGCAATAGCAGCTGCGCTTATTCTC‑TTTTCCGCGCAGGGCGTTGCGGAACAAACCACGCAGCCAGTTGTTACTTCTTGTGCCAATg  >  2:946345/1‑139 (MQ=255)

                                                                                                                             gCTAATTGAAAACGTGACAACGTCACTGAGGCAATCATGAAACCACTTTCATCCGCAATAGCAGCTGCGCTTATTCTC‑TTTTCCGCGCAGGGCGTTGCGGAACAAACCACGCAGCCAGTTGTTACTTCTTGTGCCAATg  >  1:942309/1‑139 (MQ=255)

CTTCGAGTCGCAACAAACTCTGACCCGAACCTTCAAAAATTACTTTGATGTTCCGCCGCATAAATACCGGATGACCAATATGCAGGGCGAATCGCGCTTTTTACATCCATTAAATCATTACAACAGCTAGTTGAAAACGTGACAACGTCACTGAGGCAATCATGAAACCACTTTCATCCGCAATAGCAGCTGCGCTTATTCTC‑TTTTCCGCGCAGGGCGTTGCGGAACAAACCACGCAGCCAGTTGTTACTTCTTGTGCCAATG  >  NC_000913/1619828‑1620091

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 34 ≤` `ATCG/ATCG` `< 36 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A